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UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot O95202: Variant p.Asp358Asn

Mitochondrial proton/calcium exchanger protein
Gene: LETM1
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Variant information Variant position: help 358 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant: help LP/P [Disclaimer] The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance
Residue change: help From Aspartate (D) to Asparagine (N) at position 358 (D358N, p.Asp358Asn). Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.
Physico-chemical properties: help Change from medium size and acidic (D) to medium size and polar (N) The physico-chemical property of the reference and variant residues and the change implicated.
BLOSUM score: help 1 The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page
Variant description: help In CONDMIM; homozygous patient cells show abnormal mitochondrial morphology and altered levels of components of the oxidative phosphorylation machinery; loss of function in mitochondrial potassium ion transmembrane transport; does not rescue defective proton/potassium exchange in letm1-deficient yeast. Any additional useful information about the variant.
Other resources: help Links to websites of interest for the variant.


Sequence information Variant position: help 358 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length: help 739 The length of the canonical sequence.
Location on the sequence: help IGTNNFLRFQLTMRLRSIKA D DKLIAEEGVDSLNVKELQAA The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.
Residue conservation: help The multiple alignment of the region surrounding the variant against various orthologous sequences. 
Human                         IGTNNFLRFQLTMRLRSIKADDKLIAEEGVDSLNVKELQAA

Mouse                         IGTNNFLRFQLTMRLRSIKADDKLISEEGVDSLTVKELQAA

Rat                           IGTNNFLRFQLTMRLRSIKADDKLISEEGVDSLTVKELQAA

Bovine                        IGTNNFLRFQLTMRLRSIKADDKLIAEEGVDSLNVKELQAA

Chicken                       IGTNNFLRFQLTMRLRTIKADDKMIAEEGVDSLTVKELQAA

Xenopus tropicalis            IGTNNFLRFQLTMKLRSIKADDKLIADEGLDSLTVTELQAA

Zebrafish                     IGTNNFLRFQLIMKLRAIRADDKLIAEEGVDSLTANELQAA

Drosophila                    IGTTTLLRFQLRLKLRSLATDDRVIAREGVDSLDLLELQQA
Sequence annotation in neighborhood: help The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.
TypePositionsDescription
Chain 116 – 739 Mitochondrial proton/calcium exchanger protein
Topological domain 230 – 739 Mitochondrial matrix
Domain 252 – 537 Letm1 RBD
Alternative sequence 295 – 739 Missing. In isoform 2 and isoform 3.
Mutagenesis 359 – 359 D -> A. Loss of ability to complement morphologic defects of mitochondria in letm1-deficient yeast mutant. Slightly supports growth of letm1-deficient yeast mutant on minimal essential medium.



Literature citations
Bi-allelic LETM1 variants perturb mitochondrial ion homeostasis leading to a clinical spectrum with predominant nervous system involvement.
Kaiyrzhanov R.; Mohammed S.E.M.; Maroofian R.; Husain R.A.; Catania A.; Torraco A.; Alahmad A.; Dutra-Clarke M.; Groenborg S.; Sudarsanam A.; Vogt J.; Arrigoni F.; Baptista J.; Haider S.; Feichtinger R.G.; Bernardi P.; Zulian A.; Gusic M.; Efthymiou S.; Bai R.; Bibi F.; Horga A.; Martinez-Agosto J.A.; Lam A.; Manole A.; Rodriguez D.P.; Durigon R.; Pyle A.; Albash B.; Dionisi-Vici C.; Murphy D.; Martinelli D.; Bugiardini E.; Allis K.; Lamperti C.; Reipert S.; Risom L.; Laugwitz L.; Di Nottia M.; McFarland R.; Vilarinho L.; Hanna M.; Prokisch H.; Mayr J.A.; Bertini E.S.; Ghezzi D.; Oestergaard E.; Wortmann S.B.; Carrozzo R.; Haack T.B.; Taylor R.W.; Spinazzola A.; Nowikovsky K.; Houlden H.;
Am. J. Hum. Genet. 109:1692-1712(2022)
Cited for: VARIANTS CONDMIM LYS-252 DEL; ASN-293; GLN-294; SER-300; ASN-358; PRO-380; HIS-393 AND ARG-587; CHARACTERIZATION OF VARIANTS CONDMIM LYS-252 DEL; ASN-293; GLN-294; SER-300; ASN-358; PRO-380 AND ARG-587; VARIANT LEU-305; CHARACTERIZATION OF VARIANT LEU-305; INVOLVEMENT IN CONDMIM; FUNCTION; TRANSPORTER ACTIVITY;
Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.